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At least 235 records · Page 13

Mechanism of Tyrosine-Driven Deprotonation in Photosystem II Revealed by Multiscale Simulations

Photosystem II (PSII) drives light-induced water oxidation via stepwise redox transitions of its oxygen-evolving complex (OEC), a Mn 4 Ca cluster advancing through five intermediate S-states (S 0 –S 4 ). The S 2 → S 3 transition involves a redox event in which a Mn ion donates an electron to the redox-active tyrosine YZ, coupled to deprotonation of an OEC-bound water ligand─yet the underlying coupling mechanism remains unresolved. Time-resolved serial femtosecond crystallography (TR-SFX) has revealed transient electron density shifts near the redox-active tyrosine Y Z , interpreted as sequential oxidation and reduction, with reduction initiating ∼1 μs after excitation and substantially progressed by 30 μs. However, this interpretation conflicts with kinetics from photothermal beam deflection (PBD), time-resolved X-ray absorption spectroscopy (TR-XAS), and electron paramagnetic resonance (EPR), which place electron transfer at 190–400 μs and proton transfer around 30 μs. Here, we reconcile these discrepancies using quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations. We show that oxidation of P680 and Y Z breaks the symmetry of the nearby hydrogen bonds involving water molecule W4, displacing Y Z and replicating the TR-SFX features of Y Z and Q165 observed at 1 μs. This local perturbation propagates through a hydrogen-bond network, transmitting the electrostatic signal from Y Z to the E65-E312 dyad and triggering redox-coupled deprotonation via the Cl1 channel. By 30 μs, the hydrogen-bond symmetry is restored through deprotonation of W2 (or alternatively W1), reproducing the disappearance of TR-SFX density differences around Y Z and Q165 without requiring Y Z reduction. Our proposed mechanism also gives molecular insights into the O6* density, assigning it to water reorganization rather than a discrete Ca-bound hydroxide species. Here, our results reveal a detailed atomistic mechanism linking Y Z oxidation to long-range proton release and suggest a functional role for the nearby Cl – ion in proton transfer. More broadly, this study underscores the importance of hydrogen-bond dynamics in mediating redox-driven proton transport and demonstrates how integrative simulations can resolve mechanistic ambiguities.

Deprotonation↗

Simulations of nonradiative processes in semiconductor nanocrystals

The description of carrier dynamics in spatially confined semiconductor nanocrystals (NCs), which have enhanced electron–hole and exciton–phonon interactions, is a great challenge for modern computational science. These NCs typically contain thousands of atoms and tens of thousands of valence electrons with discrete spectra at low excitation energies, similar to atoms and molecules, that converge to the continuum bulk limit at higher energies. Computational methods developed for molecules are limited to very small nanoclusters, and methods for bulk systems with periodic boundary conditions are not suitable due to the lack of translational symmetry in NCs. This perspective focuses on our recent efforts in developing a unified atomistic model based on the semiempirical pseudopotential approach, which is parameterized by first-principle calculations and validated against experimental measurements, to describe two of the main nonradiative relaxation processes of quantum confined excitons: exciton cooling and Auger recombination. Here, we focus on the description of both electron–hole and exciton–phonon interactions in our approach and discuss the role of size, shape, and interfacing on the electronic properties and dynamics for II–VI and III–V semiconductor NCs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nonlinear deformation and elasticity of BCC refractory metals and alloys

Application of isotropic pressure or uniaxial strain alters the elastic properties of materials; sufficiently large strains can drive structural transformations. Linear elasticity describes stability against infinitesimal strains, while nonlinear elasticity describes the response to finite deformations. Here, it was previously shown that uniaxial strain along [100] drives refractory metals and alloys towards mechanical instabilities. These include an extensional instability, and a symmetry-breaking orthorhombic distortion caused by a Jahn-Teller-Peierls instability that splays the cubic lattice vectors. Here we analyze these transitions in depth. Eigenvalues and eigenvectors of the Wallace tensor identify and classify linear instabilities in the presence of strain. We show that both instabilities are discontinuous, leading to discrete jumps in the lattice parameters. We provide physical intuition for the instabilities by analyzing the changes in first-principles energy, stress, bond lengths, and angles upon application of strain. Electronic band structure calculations show differential occupation of bonding and antibonding orbitals, driven by the changing bond lengths and leading to the structural transformations. Strain thresholds for these instabilities depend on the valence electron count.

36 MATERIALS SCIENCE↗

Characterizing Artificial Viscosity Parameters with Approximate Symmetries

We are often faced with trying to capture the physics of compressible shocks, which are governed by the Euler equations. However, Euler shocks are formally discontinuous at the shock front (translating to a step-function behavior of rel evant flow variables). This poses a practical problem for codes with finite-sized grid elements. As a result, one must make a concession in simulating the be havior of shocks within a discrete framework. In particular, we must blur, or ‘regularize’ Euler shocks so that they may be captured on a finite grid.

97 MATHEMATICS AND COMPUTING↗

Dirac-Harper Theory for One-Dimensional Moiré Superlattices

In this work, we study a Dirac-Harper model for moiré bilayer superlattices where layer antisymmetric strain periodically modulates the interlayer coupling between two honeycomb lattices in one spatial dimension. Discrete and continuum formulations of this model are analyzed. For a sufficiently long moiré period we find low-energy spectra that host a manifold of weakly dispersive bands arising from a hierarchy of momentum and position-dependent mass inversions. We analyze their charge distributions, mode count, and valley coherence using exact symmetries of the lattice model and approximate symmetries of a four-flavor version of the Jackiw-Rebbi one-dimensional solution.

36 MATERIALS SCIENCE↗

Rotational bands beyond the Elliott model

Rotational bands are commonplace in the spectra of atomic nuclei. Inspired by early descriptions of these bands by quadrupole deformations of a liquid drop, Elliott constructed discrete nucleon representations of SU(3) from fermionic creation and annihilation operators. Ever since, Elliott's model has been foundational to descriptions of rotation in nuclei. Later work, however, suggested the symplectic extension Sp(3, R) provides a more unified picture. We decompose no-core shell-model nuclear wave functions into symmetry-defined subspaces for several beryllium isotopes, as well as 20 Ne, using the quadratic Casimirs of both Elliott's SU(3) and Sp(3, R). The band structure, delineated by strong B(E2) values, has a more consistent description in Sp(3, R) rather than SU(3). In particular, we confirm previous work finding in some nuclides strongly connected upper and lower bands with the same underlying symplectic structure.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

AI-Assisted Conceptual Development of a Pre-Geometric Cosmological Model - An Exercise in AI-Assisted Conceptual Framework Generation, Paper III: Cosmological Structure and Predictions

This paper develops the cosmological consequences of the replication-driven cosmogenesis framework introduced in Paper I and the emergent geometric structure established in Paper II. After the replication epoch freezes out, the coherent sector occupies a finite spectral band and contains a population of excited states. The relaxation of these excited coherent configurations does not produce coherent radiation; instead, all released energy flows into the incoherent substrate, where the randomizer acts as a rapid phase-scrambling mechanism. This process generates an effectively thermal radiation bath, providing a natural reheating mechanism that requires neither inflaton oscillations nor scalar-field potentials, and can be contrasted with standard scenarios of nonperturbative reheating dynamics. Subsequent symmetry-breaking transitions in the coherent vacuum inject additional radiation, yielding a multi-stage thermal history with well-defined energy transfers. We derive the effective equations of state for each component—the cosmological vacuum, the coherent vacuum, and the radiation bath—and show how their interplay produces an FRW-like expansion. The discrete sequence of coherent-state relaxations imprints a distinctive multi-peaked stochastic gravitational-wave background, whose spectral structure reflects the underlying hierarchy of coherent frequencies. Potential observational signatures in the LISA and mid-band frequency ranges are highlighted, providing concrete avenues to test this replication-based cosmological framework in the context of standard cosmological gravitational-wave backgrounds and LISA-oriented forecasts.

79 ASTRONOMY AND ASTROPHYSICS↗

Direct Laser Writing Crystal Polymorphs of Organic Semiconductors for Phase Change Electronics

The many diverse polymorphic behaviors observed in organic electronic materials offer opportunities to modulate electronic properties through reversibly switching crystal structures. Here, we access the prolific polymorphism observed in two-dimensional quinoidal terthiophene via laser writing to locally heat and direct the phase transitions. We access a metastable polymorph IV through rapid cooling and observe distinct symmetry as well as packing through grazing incidence X-ray diffraction (GIXD). Using our open-source PolyChemPrint patterning platform, we direct laser heating to initiate the IV-I transition, switching the conductance by >2 orders of magnitude. Here, this is confirmed via a combination of GIXD and Raman spectroscopy. Finally, we demonstrate switching of transistor devices as well as discrete tuning of conductance via laser writing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Edge Reconstruction in a Quantum Spin Hall Insulator

We study interaction-driven edge reconstruction in a quantum spin Hall insulator described by the Bernevig-Hughes-Zhang model with Kanamori-Hubbard interactions using the real-space density matrix renormalization group method in both the grand-canonical and canonical ensembles. For a two-dimensional cylinder with a smooth edge, we identify discrete particle-number transitions that lead to a spin-polarized edge state stabilized by an emergent ferromagnetic exchange interaction. The reconstruction is orbital-selective, occurring predominantly in the 𝑠-orbital channel. Our results reveal a microscopic mechanism for emergent fluctuating moments at the edge that could compromise the topological protection of helical edge states by time-reversal symmetry.

Soni, Rahul [ORNL] (ORCID:0000000317714299)↗

Nodal hybridization in a two-dimensional heavy-fermion material

Metals with partially filled core atomic shells can form quasiparticles at a low temperature arising from the hybridization of the core level and conduction electrons. The thermodynamic and spectroscopic properties of these metals can be understood as those of a simple metal, but with a significant mass enhancement over the free electron mass—commonly referred to as heavy fermions. In most heavy-fermion materials, the hybridization is approximately isotropic in position and momentum space. However, a combination of low dimensionality and symmetry properties of the core-level wavefunctions can give rise to highly anisotropic electronic interactions with the conduction electrons. Here, in this study, we demonstrate anisotropic hybridization that vanishes along specific directions in momentum space—referred to as nodes—in a lanthanide-based two-dimensional van der Waals heavy-fermion compound, CeSiI. Quasiparticle interference measurements reveal a set of discrete hotspots with high spectral intensity on the Fermi surface. Theoretical modelling and comparison with the quasiparticle interference pattern of the non-heavy-fermion isostructural analogue LaSiI suggest that these features arise from an unconventional electron interaction involving hybridization nodes unique to CeSiI. As a result, the effective mass of the quasiparticles varies by orders of magnitude depending on their direction in momentum space.

36 MATERIALS SCIENCE↗

Discrete quantum geometry and intrinsic spin Hall effect

We show that the quantum geometry of the Fermi surface can be numerically described by a three-dimensional discrete quantum manifold. This approach not only avoids singularities in the Fermi sea, but it also enables the precise computation of the intrinsic Hall conductivity resolved in spin, as well as any other local properties of the Fermi surface. The method assures numerical accuracy when the Fermi level is arbitrarily close to singularities, and it remains robust when Kramers degeneracy is protected by symmetry. Furthermore, the approach is demonstrated by calculating the anomalous Hall and spin Hall conductivities of a two-band lattice model of a Weyl semimetal and a full-band ab initio model of zinc-blende GaAs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Hidden Subsurface Reconstruction and Its Atomic Origins in Layered Oxide Cathodes

Structural transformations near surfaces of solid-state materials underpin functional mechanisms of a broad range of applications including catalysis, memory, and energy storage. It has been a long-standing notion that the outmost free surfaces, accompanied by broken translational symmetry and altered atomic configurations, are usually the birthplace for structural transformations. Here, in a layered oxide cathode for Li-ion batteries, we for the first time observe the incipient state of the well documented layered-to-spinel-like structural transformation, which is surprisingly initiated from subsurface layer, rather than the very surface. Coupling atomic level scanning transmission electron microscopy imaging with electron energy loss spectroscopy, we discover that the reconstructed subsurfaces, featuring a mix of discrete patches of layered and spinel-like structures, are associated with selective atomic species partition and consequent nanoscale non-uniform composition gradient distribution at the subsurface. In conclusion, our findings provide fundamental insights on atomic-scale mechanisms of structural transformation in layered cathodes.

25 ENERGY STORAGE↗

Fermionic Partial Tomography via Classical Shadows

Here we propose a tomographic protocol for estimating any k-body reduced density matrix (k-RDM) of an n-mode fermionic state, a ubiquitous step in near-term quantum algorithms for simulating many-body physics, chemistry, and materials. Our approach extends the framework of classical shadows, a randomized approach to learning a collection of quantum-state properties, to the fermionic setting. Our sampling protocol uses randomized measurement settings generated by a discrete group of fermionic Gaussian unitaries, implementable with linear-depth circuits. We prove that estimating all k-RDM elements to additive precision ϵ requires on the order of ($^{n}_{k}$)k 3/2 log(n)/ϵ 2 repeated state preparations, which is optimal up to the logarithmic factor. Furthermore, numerical calculations show that our protocol offers a substantial improvement in constant overheads for k ≥ 2, as compared to prior deterministic strategies. We also adapt our method to particle-number symmetry, wherein the additional circuit depth may be halved at the cost of roughly 2–5 times more repetitions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

High-Order Mesh r-Adaptivity with Tangential Relaxation and Guaranteed Mesh Validity

High-order meshes are crucial for achieving optimal convergence rates in curvilinear domains, preserving symmetry, and aligning with key flow features in moving mesh simulations [1], but their quality is challenging to control. In prior work, we have developed techniques based on Target-Matrix Optimization Paradigm (TMOP) to adapt a given high-order mesh to the geometry and solution of the partial differential equation (PDE) [2, 3]. Here, we extend this framework to address two key gaps in the literature for highorder mesh 𝑟-adaptivity. First, we introduce tangential relaxation on curved surfaces using solely the discrete mesh representation, eliminating the need for access to underlying geometry (e.g., CAD model). Second, we ensure a continuously positive Jacobian determinant throughout the domain. This determinant positivity is essential for using the high-order mesh resulting from 𝑟-adaptivity with arbitrary quadrature schemes in simulations. The proposed approach is demonstrated to be robust using a variety of numerical experiments.

Mathematics and Computing↗

Trace anomaly form factors from lattice QCD

The hadron mass can be obtained through the calculation of the trace of the energy-momentum tensor in the hadron which includes the trace anomaly and sigma terms. The anomaly due to conformal symmetry breaking is believed to be an important ingredient for hadron mass generation and confinement. In this work, we will present the calculation of the glue part of the trace anomaly form factors of the pion up to Q 2 ∼ 4.3 GeV 2 and the nucleon up to Q 2 ∼ 1 GeV 2 . The calculations are performed on a domain wall fermion ensemble with overlap valence quarks at seven valence pion masses varying from ∼ 250 to ∼ 540 MeV , including the unitary point ∼ 340 MeV . We calculate the radius of the glue trace anomaly for the pion and the nucleon from the z expansion. By performing a two-dimensional Fourier transform on the glue trace anomaly form factors in the infinite momentum frame with no energy transfer, we also obtain their spatial distributions for several valence quark masses. The results are qualitatively extrapolated to the physical valence pion mass with systematic errors from the unphysical sea quark mass, discretization effects in the renormalization sum rule, and finite-volume effects to be addressed in the future. We find the pion’s form factor changes sign, as does its spatial distribution, for light quark masses. This explains how the trace anomaly contribution to the pion mass approaches zero toward the chiral limit. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

U(1) fields from qubits: An approach via D-theory algebra

A new quantum link microstructure was proposed for the lattice quantum chromodynamics (QCD) Hamiltonian, replacing the Wilson gauge links with a bilinear of fermionic qubits, later generalized to D-theory. This formalism provides a general framework for building lattice field theory algorithms for quantum computing. We focus mostly on the simplest case of a quantum rotor for a single compact U(1) field. We also make some progress for non-Abelian setups, making it clear that the ideas developed in the U(1) case extend to other groups. These in turn are building blocks for 1 + 0 -dimensional ( 1 + 0 -D) matrix models, 1 + 1 -D sigma models and non-Abelian gauge theories in 2 + 1 and 3 + 1 dimensions. By introducing multiple flavors for the U(1) field, where the flavor symmetry is gauged, we can efficiently approach the infinite-dimensional Hilbert space of the quantum O(2) rotor with increasing flavors. The emphasis of the method is on preserving the symplectic algebra exchanging fermionic qubits by sigma matrices (or hard bosons) and developing a formal strategy capable of generalization to a SU ( 3 ) field for lattice QCD and other non-Abelian 1 + 1 -D sigma models or 3 + 1 -D gauge theories. For U(1), we discuss briefly the qubit algorithms for the study of the discrete 1 + 1 -D sine-Gordon equation. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Skyrmion–skyrmion interaction in a magnetic film

Interaction of two skyrmions stabilized by the ferromagnetic exchange, Dzyaloshinskii–Moriya interaction (DMI), and external magnetic field has been studied numerically on a 2D lattice of size large compared to the separation, d, between the skyrmions. We show that two skyrmions of the same chirality (determined by the symmetry of the crystal) repel. In accordance with earlier analytical results, their long-range pair interaction falls out with the separation as exp(-d/δ H ), where δ H is the magnetic screening length, independent of the DMI. The prefactor in this expression depends on the DMI that drives the repulsion. The latter results in the spiral motion of the two skyrmions around each other, with the separation between them growing logarithmically with time. When two skyrmions of the total topological charge Q = 2 are pushed close to each other, the discreteness of the atomic lattice makes them collapse into one skyrmion of charge Q = 1 below a critical separation. Experiment is proposed that would allow one to measure the interaction between two skyrmions by holding them in positions with two magnetic tips. Our findings should be of value for designing topologically protected magnetic memory based upon skyrmions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗